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mmu_circCask_586
Basic information of circular RNA
PanCircBase ID:
mmu_circCask_586
mm39_Chr. Position ID:
chrX|13466595|13492536|-
Gene name:
Cask
Transcript:
ENSMUST00000156096.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,8377,14113,20293,25838
Genomic length:
25941
Exon/intron sizes in nt:
1,00,84,12,31,76,103
Flanking exon/introns:
chrX:13453204-13466595|chrX:13492536-13543823
Splice length:
586
Other database IDs:
circBase: mmu_circ_0016124, CIRCpedia: MMU_CIRCpedia_8346, circAtlas: mmu-Cask_0005
circBase: hsa_circ_0001916, circAtlas: hsa-CASK_0006, CIRCpedia: HSA_CIRCpedia_65862
Human Ortholog IDs:
Mature spliced Sequence:
CCCCACTGTGTTCTCCTTGCCTCAAAAGAAAACTCGGCACCTGTTAAACTTGGGGGCTTTGGGGTGGCCATTCAGTTAGGAGAATCTGGACTTGTTGCTGGAGGCCGCGTTGGAACACCTCACTTTATGGCCCCAGAAGTGGTCAAGAGAGAGCCTTACGGAAAGCCTGTGGATGTCTGGGGCTGTGGTGTGATCCTTTTCATCCTGCTCAGTGGCTGTTTGCCTTTCTACGGAACCAAGGAAAGATTGTTTGAAGGCATTATTAAAGGAAAATATAAGATGAATCCAAGGCAGTGGAGCCATATCTCTGAAAGTGCCAAAGACCTAGTACGCCGCATGCTGATGCTGGATCCTGCTGAAAGGATCACTGTTTATGAAGCACTGAATCACCCATGGCTTAAGGAGCGGGATCGTTATGCCTACAAAATCCATCTTCCAGAAACAGTAGAACAACTGAGGAAATTCAATGCAAGGAGAAAACTAAAGGGTGCAGTACTAGCTGCTGTGTCAAGTCACAAATTCAATTCCTTCTATGGGGACCCTCCTGAAGAGTTGCCAGATTTCTCCGAAGACCCTACCTCCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGTGTCAAGTCACA
59.82
CCCCAAAGCCCCCAAGTTTA
60.18
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGTGTCAAGTCACA
59.82
CCTAACTGAATGGCCACCCC
60.4
169
PCR template sequence:
GGTGCAGTACTAGCTGCTGTGTCAAGTCACAAATTCAATTCCTTCTATGGGGACCCTCCTGAAGAGTTGCCAGATTTCTCCGAAGACCCTACCTCCTCAGCCCCACTGTGTTCTCCTTGCCTCAAAAGAAAACTCGGCACCTGTTAAACTTGGGGGCTTTGGGGTGGCCATTCAGTTAGGAGAATCTGGACTTGTTGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-181a-5p(1), mmu-miR-322-5p(1), mmu-miR-33-5p(1), mmu-miR-433-5p(1), mmu-miR-96-5p(1), mmu-miR-758-3p(1), mmu-miR-338-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTACCTCCTCAGCCCCACTGTGTTC
siRNA sets
GTGGGGCTGAGGAGGTAGG, AGTGGGGCTGAGGAGGTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCASK_586_ORF_1
0.8356
0.142912656
0.814412141
639
ORF sequence:
ATGGGGACCCTCCTGAAGAGTTGCCAGATTTCTCCGAAGACCCTACCTCCTCAGCCCCACTGTGTTCTCCTTGCCTCAAAAGAAAACTCGGCACCTGTTAAACTTGGGGGCTTTGGGGTGGCCATTCAGTTAGGAGAATCTGGACTTGTTGCTGGAGGCCGCGTTGGAACACCTCACTTTATGGCCCCAGAAGTGGTCAAGAGAGAGCCTTACGGAAAGCCTGTGGATGTCTGGGGCTGTGGTGTGATCCTTTTCATCCTGCTCAGTGGCTGTTTGCCTTTCTACGGAACCAAGGAAAGATTGTTTGAAGGCATTATTAAAGGAAAATATAAGATGAATCCAAGGCAGTGGAGCCATATCTCTGAAAGTGCCAAAGACCTAGTACGCCGCATGCTGATGCTGGATCCTGCTGAAAGGATCACTGTTTATGAAGCACTGAATCACCCATGGCTTAAGGAGCGGGATCGTTATGCCTACAAAATCCATCTTCCAGAAACAGTAGAACAACTGAGGAAATTCAATGCAAGGAGAAAACTAAAGGGTGCAGTACTAGCTGCTGTGTCAAGTCACAAATTCAATTCCTTCTATGGGGACCCTCCTGAAGAGTTGCCAGATTTCTCCGAAGACCCTACCTCCTCA
Peptide sequence:
MGTLLKSCQISPKTLPPQPHCVLLASKENSAPVKLGGFGVAIQLGESGLVAGGRVGTPHFMAPEVVKREPYGKPVDVWGCGVILFILLSGCLPFYGTKERLFEGIIKGKYKMNPRQWSHISESAKDLVRRMLMLDPAERITVYEALNHPWLKERDRYAYKIHLPETVEQLRKFNARRKLKGAVLAAVSSHKFNSFYGDPPEELPDFSEDPTSS
IRESfinder result
IRESfinder score
0.507342147
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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